[petsc-users] DMPlex Halo Communication or Graph Partitioner Issue
Matthew Knepley
knepley at gmail.com
Sun Feb 26 10:24:26 CST 2023
On Sun, Feb 26, 2023 at 11:19 AM Mike Michell <mi.mike1021 at gmail.com> wrote:
> Which version of petsc you tested? With petsc 3.18.4, median duan volume
> gives the same value with petsc from DMPlexComputeCellGeometryFVM().
>
This is only an accident of the data layout. The code you sent writes over
memory in the local Fortran arrays.
Thanks,
Matt
>
>> On Sat, Feb 25, 2023 at 3:11 PM Mike Michell <mi.mike1021 at gmail.com>
>> wrote:
>>
>>> My apologies for the late follow-up. There was a time conflict.
>>>
>>> A simple example code related to the issue I mentioned is attached here.
>>> The sample code does: (1) load grid on dm, (2) compute vertex-wise control
>>> volume for each node in a median-dual way, (3) halo exchange among procs to
>>> have complete control volume values, and (4) print out its field as a .vtu
>>> file. To make sure, the computed control volume is also compared with
>>> PETSc-computed control volume via DMPlexComputeCellGeometryFVM() (see lines
>>> 771-793).
>>>
>>> Back to the original problem, I can get a proper control volume field
>>> with PETSc 3.18.4, which is the latest stable release. However, if I use
>>> PETSc from the main repo, it gives a strange control volume field.
>>> Something is certainly strange around the parallel boundaries, thus I think
>>> something went wrong with halo communication. To help understand, a
>>> comparing snapshot is also attached. I guess a certain part of my code is
>>> no longer compatible with PETSc unless there is a bug in the library. Could
>>> I get comments on it?
>>>
>>
>> I can run your example. The numbers I get for "median-dual volume" do not
>> match the "PETSc volume", and the PETSc volume is correct. Moreover, the
>> median-dual numbers change, which suggests a memory fault. I compiled it
>> using address sanitizer, and it found an error:
>>
>> Number of physical boundary edge ... 4 0
>> Number of physical and parallel boundary edge ... 4
>> 0
>> Number of parallel boundary edge ... 0 0
>> Number of physical boundary edge ... 4 1
>> Number of physical and parallel boundary edge ... 4
>> 1
>> Number of parallel boundary edge ... 0 1
>> =================================================================
>> ==36587==ERROR: AddressSanitizer: heap-buffer-overflow on address
>> 0x603000022d40 at pc 0x0001068e12a8 bp 0x7ffee932cfd0 sp 0x7ffee932cfc8
>> READ of size 8 at 0x603000022d40 thread T0
>> =================================================================
>> ==36588==ERROR: AddressSanitizer: heap-buffer-overflow on address
>> 0x60300000f0f0 at pc 0x00010cf702a8 bp 0x7ffee2c9dfd0 sp 0x7ffee2c9dfc8
>> READ of size 8 at 0x60300000f0f0 thread T0
>> #0 0x10cf702a7 in MAIN__ test.F90:657
>> #1 0x10cf768ee in main test.F90:43
>> #0 0x1068e12a7 in MAIN__ test.F90:657
>> #1 0x1068e78ee in main test.F90:43
>> #2 0x7fff6b80acc8 in start (libdyld.dylib:x86_64+0x1acc8)
>>
>> 0x60300000f0f0 is located 0 bytes to the right of 32-byte region
>> [0x60300000f0d0,0x60300000f0f0)
>> allocated by thread T0 here:
>> #2 0x7fff6b80acc8 in start (libdyld.dylib:x86_64+0x1acc8)
>>
>> 0x603000022d40 is located 0 bytes to the right of 32-byte region
>> [0x603000022d20,0x603000022d40)
>> allocated by thread T0 here:
>> #0 0x114a7457f in wrap_malloc (libasan.5.dylib:x86_64+0x7b57f)
>> #1 0x1068dba71 in MAIN__ test.F90:499
>> #2 0x1068e78ee in main test.F90:43
>> #3 0x7fff6b80acc8 in start (libdyld.dylib:x86_64+0x1acc8)
>>
>> SUMMARY: AddressSanitizer: heap-buffer-overflow test.F90:657 in MAIN__
>> Shadow bytes around the buggy address:
>>
>> which corresponds to
>>
>> ! midpoint of median-dual face for inner face
>> axrf(ifa,1) = 0.5d0*(yc(nc1)+yfc(ifa)) ! for nc1 cell
>> axrf(ifa,2) = 0.5d0*(yc(nc2)+yfc(ifa)) ! for nc2 cell
>>
>> and these were allocated here
>>
>> allocate(xc(ncell))
>> allocate(yc(ncell))
>>
>> Hopefully the error is straightforward to see now.
>>
>> Thanks,
>>
>> Matt
>>
>>
>>> Thanks,
>>> Mike
>>>
>>>
>>>> On Mon, Feb 20, 2023 at 12:05 PM Matthew Knepley <knepley at gmail.com>
>>>> wrote:
>>>>
>>>>> On Sat, Feb 18, 2023 at 12:00 PM Mike Michell <mi.mike1021 at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> As a follow-up, I tested:
>>>>>>
>>>>>> (1) Download tar for v3.18.4 from petsc gitlab (
>>>>>> https://gitlab.com/petsc/petsc/-/tree/v3.18.4) has no issue on
>>>>>> DMPlex halo exchange. This version works as I expect.
>>>>>> (2) Clone main branch (git clone https://gitlab.com/petsc/petsc.git)
>>>>>> has issues with DMPlex halo exchange. Something is suspicious about this
>>>>>> main branch, related to DMPlex halo. The solution field I got is not
>>>>>> correct. But it works okay with 1-proc.
>>>>>>
>>>>>> Does anyone have any comments on this issue? I am curious if other
>>>>>> DMPlex users have no problem regarding halo exchange. FYI, I do not
>>>>>> declare ghost layers for halo exchange.
>>>>>>
>>>>>
>>>>> There should not have been any changes there and there are definitely
>>>>> tests for this.
>>>>>
>>>>> It would be great if you could send something that failed. I could fix
>>>>> it and add it as a test.
>>>>>
>>>>
>>>> Just to follow up, we have tests of the low-level communication (Plex
>>>> tests ex1, ex12, ex18, ex29, ex31), and then we have
>>>> tests that use halo exchange for PDE calculations, for example SNES
>>>> tutorial ex12, ex13, ex62. THe convergence rates
>>>> should be off if the halo exchange were wrong. Is there any example
>>>> similar to your code that is failing on your installation?
>>>> Or is there a way to run your code?
>>>>
>>>> Thanks,
>>>>
>>>> Matt
>>>>
>>>>
>>>>> Thanks,
>>>>>
>>>>> Matt
>>>>>
>>>>>
>>>>>> Thanks,
>>>>>> Mike
>>>>>>
>>>>>>
>>>>>>> Dear PETSc team,
>>>>>>>
>>>>>>> I am using PETSc for Fortran with DMPlex. I have been using this
>>>>>>> version of PETSc:
>>>>>>> >>git rev-parse origin
>>>>>>> >>995ec06f924a86c4d28df68d1fdd6572768b0de1
>>>>>>> >>git rev-parse FETCH_HEAD
>>>>>>> >>9a04a86bf40bf893fb82f466a1bc8943d9bc2a6b
>>>>>>>
>>>>>>> There has been no issue, before the one with VTK viewer, which Jed
>>>>>>> fixed today (
>>>>>>> https://gitlab.com/petsc/petsc/-/merge_requests/6081/diffs?commit_id=27ba695b8b62ee2bef0e5776c33883276a2a1735
>>>>>>> ).
>>>>>>>
>>>>>>> Since that MR has been merged into the main repo, I pulled the
>>>>>>> latest version of PETSc (basically I cloned it from scratch). But if I use
>>>>>>> the same configure option with before, and run my code, then there is an
>>>>>>> issue with halo exchange. The code runs without error message, but it gives
>>>>>>> wrong solution field. I guess the issue I have is related to graph
>>>>>>> partitioner or halo exchange part. This is because if I run the code with
>>>>>>> 1-proc, the solution is correct. I only updated the version of PETSc and
>>>>>>> there was no change in my own code. Could I get any comments on the issue?
>>>>>>> I was wondering if there have been many changes in halo exchange or graph
>>>>>>> partitioning & distributing part related to DMPlex.
>>>>>>>
>>>>>>> Thanks,
>>>>>>> Mike
>>>>>>>
>>>>>>
>>>>>
>>>>> --
>>>>> What most experimenters take for granted before they begin their
>>>>> experiments is infinitely more interesting than any results to which their
>>>>> experiments lead.
>>>>> -- Norbert Wiener
>>>>>
>>>>> https://www.cse.buffalo.edu/~knepley/
>>>>> <http://www.cse.buffalo.edu/~knepley/>
>>>>>
>>>>
>>>>
>>>> --
>>>> What most experimenters take for granted before they begin their
>>>> experiments is infinitely more interesting than any results to which their
>>>> experiments lead.
>>>> -- Norbert Wiener
>>>>
>>>> https://www.cse.buffalo.edu/~knepley/
>>>> <http://www.cse.buffalo.edu/~knepley/>
>>>>
>>>
>>
>> --
>> What most experimenters take for granted before they begin their
>> experiments is infinitely more interesting than any results to which their
>> experiments lead.
>> -- Norbert Wiener
>>
>> https://www.cse.buffalo.edu/~knepley/
>> <http://www.cse.buffalo.edu/~knepley/>
>>
>
--
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener
https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
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